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Sat, Jul 20, 22:58

lammps2pdb.pl
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#!/usr/bin/perl
#
# program: lammps2pdb.pl
# author: Pieter J. in 't Veld
# pjintve@sandia.gov, veld@verizon.net
# date: September 3-4, 2004, April 23-25, 2005.
# purpose: Translation of lammps output into pdb format for use in
# conjunction with vmd
#
# Notes: Copyright by author for Sandia National Laboratories
# 20040903 Conception date of v1.0: rudimentary script for collagen
# project.
# 20050423 Conception date of v2.0:
# - changed data access through indexing data directly on disk;
# - added all command line options
# 20050425 Corrected focussing to use a target molecule's moment of
# inertia to determine its principal axis: for computational
# ease, a 3D orientational vector is calculated from two 2D
# projections
# 20050701 Changed create_names() to loosen mass recognition criterion and
# corrected created_atom_ids() to properly deal with the end of
# the data stream.
# subroutines
sub test
{
my $name = shift(@_);
printf("Error: file %s not found\n", $name) if (!scalar(stat($name)));
return !scalar(stat($name));
}
sub initialize
{
my $k = 0;
my @options = ("-help", "-nstart", "-dn", "-cut", "-repair",
"-units", "-quiet", "-nodetect", "-data", "-pbc",
"-focus", "-center", "-exclude");
my @remarks = ("display this message",
"starting frame [-1]",
"frames to skip when creating multiple frames [0]",
"cut bonds crossing over box edge [off]",
"repair bonds [off]",
"dump file entries have units [off]",
"turn display information off",
"turn auto-detection of masses off",
"use data file other than project.data",
"apply periodic boundary to molecules []",
"molecules to focus on []",
"molecules to use as center of mass []",
"exclude molecules from output []");
my @notes = (
"* Multiple frames are processed when dn > 0.",
"* Only the last frame is converted when nstart < 0.",
"* Focussing superceedes centering.",
"* Focussing uses the moment of inertia to determine the molecules'",
" principal axis; the molecules are rotated and translated to the lab",
" frame, using the focus molecules as reference.",
"* Expected files in current directory: project.data, project.dump",
"* Generated output files: project_trj.psf, project_trj.pdb",
"* Uses project_ctrl.psf if available");
$program = "lammps2pdb";
$version = "2.2.5";
$year = "2007";
$cut = 0;
$repair = 0;
$units = 0;
$info = 1;
$nstart = -1;
$dn = 0;
$detect = 1;
foreach (@ARGV)
{
if (substr($_, 0, 1) eq "-")
{
my $k = 0;
my @arg = split("=");
my $switch = (($arg[1] eq "")||($arg[1] eq "on")||($arg[1]!=0));
$arg[0] = lc($arg[0]);
foreach (@options)
{
last if ($arg[0] eq substr($_, 0, length($arg[0])));
++$k;
}
$help = 1 if (!$k--);
$nstart = $arg[1] if (!$k--);
$dn = $arg[1] if (!$k--);
$cut = $switch if (!$k--);
$repair = $switch if (!$k--);
$units = $switch if (!$k--);
$info = $switch ? 0 : 1 if (!$k--);
$detect = $switch ? 0 : 1 if (!$k--);
$data_name = $arg[1] if (!$k--);
if (!$k--) {
if ($switch) { $pbc{ALL} = 1; }
else { foreach (split(",",$arg[1])) { $pbc{uc($_)} = 1; }}}
if (!$k--) { foreach (split(",",$arg[1])) { $focus{uc($_)} = uc($_);}}
if (!$k--) { foreach (split(",",$arg[1])) { $center{uc($_)} = uc($_);}}
if (!$k--) { foreach (split(",",$arg[1])) { $exclude{uc($_)}=uc($_);}}
}
else { $project = $_ if (!$k++); }
}
if (($k<1)||$help)
{
printf("%s v%s (c)%s by Pieter J. in \'t Veld for SNL\n\n",
$program, $version, $year);
printf("Usage:\n %s.pl [-option[=#] ..] project\n\n", $program);
printf("Options:\n");
for (my $i=0; $i<scalar(@options); ++$i)
{
printf(" %-10.10s %s\n", $options[$i], $remarks[$i]);
}
printf("\nNotes:\n") if (scalar(@notes));
foreach(@notes) { printf(" %s\n", $_); };
printf("\n");
exit(-1);
}
printf("%s v%s (c)%s\n\n", $program, $version, $year) if ($info);
$data_name = $project.".data" if ($data_name eq "");
$traject_name = $project.".dump";
$pdb_name = $project."_trj.pdb";
$psf_name = $project."_trj.psf";
$psf_ctrl_name = $project."_ctrl.psf";
$psf_ctrl = scalar(stat($psf_ctrl_name));
$traject_flag = scalar(stat($traject_name));
my $flag = test($data_name);
printf("Conversion aborted\n\n") if ($flag);
exit(-1) if ($flag);
# data input
create_atom_ids();
create_bonds();
open(TRAJECT, "<".$traject_name) if ($traject_flag);
open(PSF_CTRL, "<".$psf_ctrl_name) if ($psf_ctrl);
# open output
open(PSF, ">".$psf_name) if (!$psf_ctrl);
open(PDB, ">".$pdb_name);
# align center with focus
%center = %focus if (scalar(%focus));
}
# Vector routines
sub V_String # V_String(@a)
{
return "{".join(", ", @_)."}";
}
sub V_Round
{
foreach(@_) { $_ = ($_<0 ? -int(-$_*1e11+0.5) : int($_*1e11+0.5))/1e11; }
return @_;
}
sub V_Add # V_Add(@a, @b) = @a + @b;
{
return (@_[0]+@_[3], @_[1]+@_[4], @_[2]+@_[5]);
}
sub V_Subtr # V_Subtr(@a, @b) = @a - @b;
{
return (@_[0]-@_[3], @_[1]-@_[4], @_[2]-@_[5]);
}
sub V_Dot # V_Dot(@a, @b) = @a . @b;
{
return (@_[0]*@_[3]+@_[1]*@_[4]+@_[2]*@_[5]);
}
sub V_Cross # V_Cross(@a, @b) = @a x @b;
{
return (@_[1]*@_[5]-@_[2]*@_[4], @_[2]*@_[3]-@_[0]*@_[5],
@_[0]*@_[4]-@_[1]*@_[3]);
}
sub V_Mult # V_Mult($f, @a) = $f * @a;
{
return (@_[0]*@_[1], @_[0]*@_[2], @_[0]*@_[3]);
}
sub V_Norm # V_Norm(@a) = @a/|@a|;
{
return V_Mult(1/sqrt(V_Dot(@_[0,1,2],@_[0,1,2])), @_[0,1,2]);
}
sub pbc # periodic -0.5*L <= x < 0.5*L
{
my $x = @_[0]/@_[1]+0.5;
return @_[0]-@_[1]*($x<0 ? int($x)-1 : int($x));
}
sub V_PBC # V_PBC(@a, @l)
{
return (pbc(@_[0], @_[3]), pbc(@_[1], @_[4]), pbc(@_[2], @_[5]));
}
sub V_Cmp # V_Cmp(abs(@a), abs(@b))
{
return -1 if (abs($_[0])<abs($_[3]));
return 1 if (abs($_[0])>abs($_[3]));
return -1 if (abs($_[1])<abs($_[4]));
return 1 if (abs($_[1])>abs($_[4]));
return -1 if (abs($_[2])<abs($_[5]));
return 1 if (abs($_[2])>abs($_[5]));
return 0;
}
sub V_Sort # sort on descending absolute
{ # value
my @v = @_;
for (my $i=0; $i<scalar(@v)-3; $i+=3)
{
for (my $j=$i+3; $j<scalar(@v); $j+=3)
{
my @u = @v[$i, $i+1, $i+2];
next if (V_Cmp(@u, @v[$j, $j+1, $j+2])>=0);
@v[$i,$i+1,$i+2]= @v[$j,$j+1,$j+2];
@v[$j,$j+1,$j+2]= @u;
}
}
return @v;
}
# Matrix routines
sub M_String # M_String(@A)
{
my @M;
for (my $i=0; $i<3; ++$i) { push(@M, V_String(splice(@_, 0, 3))); }
return "{".join(", ", @M)."}";
}
sub M_Round
{
return V_Round(@_);
}
sub M_Transpose # M_Transpose(@A) = (@A)^t;
{
return (@_[0], @_[3], @_[6], @_[1], @_[4], @_[7], @_[2], @_[5], @_[8]);
}
sub M_Dot # M_Dot(@A, @B) = @A . @B;
{
return (
V_Dot(@_[0,1,2], @_[ 9,12,15]), V_Dot(@_[0,1,2], @_[10,13,16]),
V_Dot(@_[0,1,2], @_[11,14,17]),
V_Dot(@_[3,4,5], @_[ 9,12,15]), V_Dot(@_[3,4,5], @_[10,13,16]),
V_Dot(@_[3,4,5], @_[11,14,17]),
V_Dot(@_[6,7,8], @_[ 9,12,15]), V_Dot(@_[6,7,8], @_[10,13,16]),
V_Dot(@_[6,7,8], @_[11,14,17]));
}
sub M_Det # M_Det(@A) = | @A |
{
return V_Dot(@_[0,1,2], V_Cross(@_[3,4,5], @_[6,7,8]));
}
sub M_Mult # M_Mult($a, @A) = $a * @A
{
return (
@_[0]*@_[1], @_[0]*@_[2], @_[0]*@_[3],
@_[0]*@_[4], @_[0]*@_[5], @_[0]*@_[6],
@_[0]*@_[7], @_[0]*@_[8], @_[0]*@_[9]);
}
sub M_Unit { return (1,0,0, 0,1,0, 0,0,1); }
sub PI { return 4*atan2(1,1); }
sub M_Rotate # M_Rotate($n, $alpha) = @R_$n;
{ # vmd convention
my $n = shift(@_);
my $alpha = shift(@_)*PI()/180;
my $cos = cos($alpha);
my $sin = sin($alpha);
$cos = 0 if (abs($cos)<1e-16);
$sin = 0 if (abs($sin)<1e-16);
return (1,0,0, 0,$cos,-$sin, 0,$sin,$cos) if ($n==0); # around x-axis
return ($cos,0,$sin, 0,1,0, -$sin,0,$cos) if ($n==1); # around y-axis
return ($cos,-$sin,0, $sin,$cos,0, 0,0,1) if ($n==2); # around z-axis
return M_Unit();
}
sub M_RotateNormal # returns R.(1,0,0) = @a/|@a|;
{
my @R = M_Unit();
my @n = V_Mult(1.0/sqrt(V_Dot(@_[0,1,2], @_)), @_);
my $sina = $n[1]<0 ? -sqrt($n[1]*$n[1]+$n[2]*$n[2]) :
sqrt($n[1]*$n[1]+$n[2]*$n[2]);
if ($sina)
{
my $cosa = $n[0];
my $cosb = $n[1]/$sina;
my $sinb = $n[2]/$sina;
@R = (
$cosa ,-$sina , 0,
$cosb*$sina, $cosb*$cosa, -$sinb,
$sinb*$sina, $sinb*$cosa, $cosb);
}
return @R;
}
sub MV_Dot # MV_Dot(@A, @b) = @A . @b;
{
return (V_Dot(@_[0,1,2], @_[9,10,11]), V_Dot(@_[3,4,5], @_[9,10,11]),
V_Dot(@_[6,7,8], @_[9,10,11]));
}
sub M_Sweep
{
my @M = @_;
for (my $i=0; $i<3; ++$i)
{
@M = V_Sort(@M);
my @v = splice(@M, 3*$i, 3);
if (abs($v[$i])>1e-10)
{
@v = V_Mult(1/$v[$i], @v);
@M[0,1,2] = V_Subtr(@M[0,1,2], V_Mult($M[$i], @v));
@M[3,4,5] = V_Subtr(@M[3,4,5], V_Mult($M[$i+3], @v));
}
@M = (@v, @M) if ($i==0);
@M = (@M[0,1,2], @v, @M[3,4,5]) if ($i==1);
@M = (@M, @v) if ($i==2);
}
return V_Round(@M);
}
# Complex routines
sub C_Add # z = z1 + z2
{
return (@_[0]+@_[2], @_[1]+@_[3]);
}
sub C_Subtr # z = z1 - z2
{
return (@_[0]-@_[2], @_[1]-@_[3]);
}
sub C_Mult # z = z1 * z2
{
return (@_[0]*@_[2]-@_[1]*@_[3], @_[0]*@_[3]+@_[2]*@_[1]);
}
sub C_Div # z = z1 / z2
{
my $num = @_[2]*@_[2]+@_[3]*@_[3];
return ((@_[0]*@_[2]+@_[1]*@_[3])/$num, (@_[1]*@_[2]-@_[0]*@_[3])/$num);
}
sub C_Pow # z = z1 ^ a
{
my $r = (sqrt(@_[0]*@_[0]+@_[1]*@_[1]))**@_[2];
my $a = @_[2]*atan2(@_[1], @_[0]);
return ($r*cos($a), $r*sin($a));
}
sub C_Correct
{
return (abs(@_[0])<1e-14 ? 0 : @_[0], abs(@_[1])<1e-14 ? 0 : @_[1]);
}
sub C_Zero
{
return (abs(@_[0])<1e-8 ? 0 : @_[0], abs(@_[1])<1e-8 ? 0 : @_[1]);
}
sub C_Conj
{
return (@_[0], -@_[1]);
}
sub C_String
{
return @_[0]." + ".@_[1]."i";
}
# analytical roots
sub R_Sort
{
my $n = scalar(@_);
for (my $i=0; $i<$n-2; $i+=2)
{
for (my $j=$i+2; $j<$n; $j+=2)
{
if (@_[$j]<@_[$i]) {
my @t = @_[$i,$i+1]; @_[$i,$i+1] = @_[$j,$j+1]; @_[$j,$j+1] = @t; }
else { if ((@_[$j]==@_[$i])&&(@_[$j+1]<@_[$i+1])) {
my @t = @_[$i,$i+1]; @_[$i,$i+1] = @_[$j,$j+1]; @_[$j,$j+1] = @t; } }
}
}
return @_;
}
sub R_First
{
return (0, 0) if (abs(@_[1])<1e-14);
return (-@_[0]/@_[1], 0);
}
sub R_Second
{
return R_First(@_) if (abs(@_[2]<1e-14));
my @z = (-@_[1]/@_[2]/2.0, 0);
my @root = C_Correct(C_Pow(($z[0]*$z[0]-@_[0]/@_[2], 0), 1/2));
return (C_Zero(C_Subtr(@z, @root)), C_Zero(C_Add(@z, @root)));
}
sub R_Third
{
return R_Second(@_) if (abs(@_[3])<1e-14);
my $c3 = 3*@_[3];
my $f1 = @_[1]*$c3-@_[2]*@_[2];
my $f2 = 0.5*@_[2]*(3*$f1+@_[2]*@_[2])-1.5*@_[0]*$c3*$c3;
my $f3 = -@_[2]/$c3;
my @A = (0, 0);
my @B = (0, 0);
my @z1 = (0.5, 0.5*sqrt(3));
my @z2 = C_Conj(@z1);
if (abs($f1)<1e-3) { # limit f1 -> 0
@A = ($f2<0 ? abs(2*$f2)**(1/3) : 0, 0); }
else {
if (abs($f2)<1e-14) { # limit f2 -> 0
my $f = sqrt(abs($f1))/$c3;
@A = $f1<0 ? (-$f*$z1[1], 0.5*$f) : ($f, 0);
@B = $f1<0 ? (-$A[0], $A[1]) : ($f, 0); }
else {
@B = C_Pow(C_Add(($f2, 0),
C_Pow(($f1*$f1*$f1+$f2*$f2, 0), 1/2)), 1/3);
@A = C_Div(($f1/$c3, 0), @B);
@B = ($B[0]/$c3, $B[1]/$c3); } }
return R_Sort(
C_Zero(C_Add(($f3, 0), C_Subtr(C_Mult(@z1, @A), C_Mult(@z2, @B)))),
C_Zero(C_Add(($f3, 0), C_Subtr(C_Mult(@z2, @A), C_Mult(@z1, @B)))),
C_Zero(C_Add(($f3, 0), C_Subtr(@B, @A))));
}
# general read file operators
sub advance_read
{
my $input = shift;
my $dlines = shift;
my $read;
while ($dlines--) { $read = <$input>; }
return $read;
}
sub rewind_read
{
my $input = shift;
seek($input, 0, SEEK_SET);
}
# create crossreference tables
sub create_psf_index # make an index of id
{ # locations
my @psf_ids = ("!NATOM","!NBOND:","!NTHETA:","!NPHI:","!NIMPHI:");
my @ids = (atoms, bonds, angles, dihedrals, impropers);
my $k = 0;
my %hash;
printf("Info: creating PSF index\n") if ($info);
foreach (@psf_ids) { $hash{$_} = shift(@ids); };
seek(PSF_CTRL, 0, SEEK_SET);
while (<PSF_CTRL>)
{
chop();
my @tmp = split(" ");
my $n = $hash{$tmp[1]};
$PSFIndex{$n} = tell(PSF_CTRL)." ".$tmp[0] if ($n ne "");
}
}
sub psf_goto # goto $ident in <PSF>
{
create_psf_index() if (!scalar(%PSFIndex));
my $id = shift(@_);
my @n = split(" ", $PSFIndex{$id});
@PSFBuffer = ();
if (!scalar(@n))
{
printf("Warning: PSF index for $id not found\n");
seek(PSF_CTRL, 0, SEEK_END);
return -1;
}
seek(PSF_CTRL, $n[0], SEEK_SET);
return $n[1];
}
sub psf_get
{
@PSFBuffer = split(" ", <PSF_CTRL>) if (!scalar(@PSFBuffer));
return splice(@PSFBuffer, 0, shift(@_));
}
sub create_data_index
{
my $init = 3;
my @tmp;
my $id;
my %hash;
my %size;
foreach ((masses,atoms,bonds,angles,dihedrals,impropers)) { $hash{$_}=$_; }
open(DATA, "<".$data_name);
for (my $i=0; $i<2; ++$i) { my $tmp = <DATA>; } # skip first two lines
while ($init&&!eof(DATA)) # interpret header
{
@tmp = split(" ", <DATA>);
--$init if (!scalar(@tmp));
foreach (@tmp) { $_ = lc($_); }
$tmp[1] = masses if ($tmp[1]." ".$tmp[2] eq "atom types");
$L[0] = $tmp[0]." ".($tmp[1]-$tmp[0])
if (join(" ",@tmp[2,3]) eq "xlo xhi");
$L[1] = $tmp[0]." ".($tmp[1]-$tmp[0])
if (join(" ",@tmp[2,3]) eq "ylo yhi");
$L[2] = $tmp[0]." ".($tmp[1]-$tmp[0])
if (join(" ",@tmp[2,3]) eq "zlo zhi");
if (($id = $hash{$tmp[1]}) ne "") { $size{$id} = $tmp[0]; }
}
@l = ();
for (my $i=0; $i<3; ++$i)
{
@tmp = split(" ", $L[$i]);
$l[$i] = $tmp[0];
$l[$i+3] = $tmp[1];
}
while (!eof(DATA)) # interpret data
{
@tmp = split(" ", <DATA>);
my $skip = <DATA> if (($id = $hash{lc($tmp[0])}) ne "");
$DATAIndex{$id} = tell(DATA)." ".$size{$id} if ($id ne "");
}
}
sub goto_data
{
create_data_index() if (!scalar(%DATAIndex));
my $id = shift(@_);
my @n = split(" ", $DATAIndex{$id});
if (!scalar(@n))
{
printf("Warning: DATA index for $id not found\n");
seek(DATA, 0, SEEK_END);
return -1;
}
seek(DATA, $n[0], SEEK_SET);
return $n[1];
}
# create atom and residue identifiers
sub create_names
{
return if (scalar(@names));
my $n = goto_data(masses);
my @mass = (1, 12, 14, 16, 32.1, 4, 20.2, 40.1, 65.4,
55.8, 31, 35.5, 23, 24.3, 39.1, 28.1);
my @name = ("H", "C", "N", "O", "S", "HE", "NE", "CA",
"ZN", "FE", "P", "CL", "NA", "MG", "K", "SI");
my @unknown = ("X", "Y", "Z");
my @letter = ("X", "Y", "Z", "P", "Q", "R", "S", "A", "B", "C");
my $k = 0;
my %atom;
$names[0] = "";
foreach (@mass) { $atom{$_} = shift(@name); }
for (my $i=1; $i<=$n; ++$i)
{
my @tmp = split(" ", <DATA>);
my $j = $tmp[0];
$tmp[1] = int($tmp[1]*10+0.5)/10;
if ((($names[$j] = $atom{$masses[$j] = $tmp[1]}) eq "")||!$detect)
{
$names[$j] = $letter[$k].$unknown[0];
if (++$k>9) { $k = 0; shift(@unknown); }
}
}
}
sub create_position
{
my @data = @_;
my $p = $data[1]." ".$data[2];
my $k;
for ($k=0; ($k<scalar(@data))&&(substr($data[$k],0,1) ne "#"); ++$k) { }
@data = splice(@data, $k-($k<8 ? 3 : 6), $k<8 ? 3 : 6);
foreach (@L)
{
my @l = split(" ");
$p = join(" ", $p, ($data[0]-$l[0])/$l[-1]+$data[3]);
shift(@data);
}
return $p;
}
sub create_atom_ids
{
my $res = 0;
my $last = 1;
my @data;
my $n;
my $k;
my $tmp;
my $id;
my %link;
my %special;
printf("Info: creating atom ids\n") if ($info);
create_names();
$n = goto_data(atoms);
foreach ((CL, NA, MG, K)) { $special{$_} = "ION"; }
$special{"H H O"} = "HOH";
for (my $i=0; $i<=$n; ++$i)
{
@data = split(" ", <DATA>) if ($i<$n);
$traject[$i] = create_position(@data) if ($i<$n); # positions
if ($i<$n ? ($mol[$i+1] = $data[1])!=$last : 1) # residues
{
if ((($tmp = $link{$id = join(" ", sort(split(" ", $id)))}) eq "")&&
(($tmp = $special{$id}) eq ""))
{
$link{$id} =
$tmp = "R".($res<10 ? "0" : "").$res;
++$res;
}
$cluster[$last] = "PROT";
$cluster[$last] = "WATR" if ($tmp eq "HOH");
$cluster[$last] = "SALT" if ($tmp eq "ION");
$residue[$last] = $tmp;
$last = $data[1];
$id = "";
}
$id = join(" ", $id, $names[$data[2]]);
}
}
sub crossover
{
my @d = V_Subtr((split(" ", $position[@_[0]]))[0,1,2],
(split(" ", $position[@_[1]]))[0,1,2]);
$d[0] /= $l[3];
$d[1] /= $l[4];
$d[2] /= $l[5];
return (($d[0]<-0.5)||($d[0]>=0.5)||($d[1]<-0.5)||($d[1]>=0.5)||
($d[2]<-0.5)||($d[2]>=0.5));
}
sub delete_crossovers
{
my $n = scalar(@bonds);
my $i = 0;
printf("Info: deleting crossover bonds\n") if ($info);
while ($i<$n) # take out crossovers
{
if (crossover(split(" ", $bonds[$i]))) { splice(@bonds, $i, 1); --$n; }
else { ++$i; }
}
}
sub delete_exclude
{
my $n = scalar(@bonds);
my $i = 0;
printf("Info: deleting excluded bonds\n") if ($info);
while ($i<$n)
{
my $m = $mol[(split(" ", $bonds[$i]))[0]+1];
if (($exclude{$m} ne "")||($exclude{$residue[$m]} ne "")
||($exclude{$cluster[$m]} ne "")) { splice(@bonds, $i, 1); --$n; }
else { ++$i; }
}
}
sub create_bonds
{
my $n = goto_data(bonds);
printf("Info: creating bonds\n") if ($info);
for (my $i=0; $i<$n; ++$i)
{
my @arg = split(" ", <DATA>);
$bonds[$i] = ($arg[2]-1)." ".($arg[3]-1);
}
}
# traject operators
sub advance_traject
{
my $subject = "item: ".lc(shift(@_));
my $advance = 1;
while (!eof(TRAJECT)&&(substr(lc(join(" ", split(" ", <TRAJECT>))),
0,length($subject)) ne $subject)) {}
}
sub read_traject
{
my @box;
my @l;
advance_traject("timestep");
my $timestep = (split(" ", <TRAJECT>))[0];
advance_traject("number of atoms");
my $n = (split(" ", <TRAJECT>))[0];
advance_traject("box bounds");
for (my $i=0; $i<3; ++$i)
{
my @data = split(" ", <TRAJECT>);
$box[$i] = $data[0]; # box edge
$l[$i] = $data[1]-$data[0]; # box length
}
advance_traject("atoms");
for (my $i=0; $i<$n; ++$i)
{
my @data = split(" ", <TRAJECT>); # read data
$traject[$data[0]-1] = join(" ", @data); # store data in order
}
return ($timestep, $n, @box, @l);
}
# pdb format
sub eigen_vector # eigen_vector(@A, $l)
{
my @A = splice(@_,0,9);
my $l = shift(@_);
$A[0] -= $l;
$A[4] -= $l;
$A[8] -= $l;
@A = M_Sweep(@A);
return V_Norm(-$A[2], -$A[5], 1) if (($A[0]==1)&&($A[4]==1));
return V_Norm(-$A[1], 1, -$A[7]) if (($A[0]==1)&&($A[8]==1));
return V_Norm(1, -$A[3], -$A[6]) if (($A[4]==1)&&($A[8]==1));
return (1,0,0) if ($A[0]==1);
return (0,1,0) if ($A[4]==1);
return (0,0,1) if ($A[8]==1);
return (0,0,0);
}
sub pdb_inertia
{
my @s = (
@_[3]-@_[0]*@_[0], @_[4]-@_[1]*@_[1], @_[5]-@_[2]*@_[2],
@_[6]-@_[0]*@_[1], @_[7]-@_[0]*@_[2], @_[8]-@_[1]*@_[2]);
my @c = (
($s[0]+$s[1])*(($s[0]+$s[2])*($s[1]+$s[2])-$s[3]*$s[3]) # c0
-$s[5]*($s[3]*$s[4]+($s[1]+$s[2])*$s[5])
-$s[4]*(($s[0]+$s[2])*$s[4]+$s[3]*$s[5]),
-($s[0]+$s[2])*($s[1]+$s[2])-($s[0]+$s[1])*($s[0]+$s[1]+2*$s[2]) # c1
+$s[3]*$s[3]+$s[4]*$s[4]+$s[5]*$s[5],
2*($s[0]+$s[1]+$s[2]), # c2
-1); # c3
my @sol = R_Third(@c);
my @M = ($s[1]+$s[2], -$s[3], -$s[4],
-$s[3], $s[0]+$s[2], -$s[5],
-$s[4], -$s[5], $s[0]+$s[1]);
my @a = eigen_vector(@M, $sol[0]);
my @b = eigen_vector(@M, $sol[2]);
my @A = M_Transpose(M_RotateNormal(@a));
my @B = M_Dot(M_RotateNormal(0,1,0),
M_Transpose(M_RotateNormal(MV_Dot(@A,@b))));
return M_Dot(@B, @A);
}
sub pdb_focus # using moment of inertia
{
my @R = pdb_inertia(@_);
printf("Info: focussing\n") if ($info);
foreach (@position)
{
my @p = split(" ");
$_ = join(" ", MV_Dot(@R, @p[0,1,2]), @p[3,4]);
}
}
sub pdb_center
{
my @c = splice(@_, 0, 3);
printf("Info: centering\n") if ($info);
@l[0,1,2] = V_Mult(-1/2, @l[3,4,5]);
foreach (@position)
{
my @p = split(" ");
$_ = join(" ", V_Subtr(@p[0,1,2], @c), @p[3,4]);
}
}
sub pdb_pbc
{
printf("Info: applying periodicity\n") if ($info);
foreach (@position)
{
my @p = split(" ");
my $m = $mol[$p[3]];
$_ = join(" ", V_PBC(@p[0,1,2], @l[3,4,5]), @p[3,4])
if ($pbc{ALL}||$pbc{$m}||$pbc{$residue[$m]}||$pbc{$cluster[$m]});
}
}
sub pdb_repair_bonds
{
return if (!$pbc);
printf("Info: repairing bonds\n") if ($info);
foreach (@bonds)
{
my @b = split(" ");
my @p = split(" ", $position[$b[0]]);
my @q = split(" ", $position[$b[1]]);
$position[$b[1]] = join(" ", V_Add(@p[0,1,2], V_PBC(
V_Subtr(@q[0,1,2], @p[0,1,2]), @l[3,4,5])), @q[3,4]);
}
}
sub pdb_positions
{
my @m = (0,0,0,0,0,0,0,0,0);
my $nmass = 0;
my $i = 0;
my $mass;
my @p;
my $d;
foreach (@traject)
{
my @arg = split(" ");
my $m = $mol[$arg[0]];
next if (($exclude{$m} ne "")||($exclude{$residue[$m]} ne "")
||($exclude{$cluster[$m]} ne ""));
if ($units)
{
$p[0] = $arg[2]+$arg[5]*$l[3];
$p[1] = $arg[3]+$arg[6]*$l[4];
$p[2] = $arg[4]+$arg[7]*$l[5];
}
else
{
$p[0] = $l[0]+($arg[2]+$arg[5])*$l[3];
$p[1] = $l[1]+($arg[3]+$arg[6])*$l[4];
$p[2] = $l[2]+($arg[4]+$arg[7])*$l[5];
}
$position[$i++] = join(" ", @p, $arg[0], $arg[1]);
next if (($center{$m} eq "")&&($center{$cluster[$m]} eq ""));
$nmass += $mass = $masses[$arg[1]]; # inertia necessities:
$m[0] += $d = $mass*$p[0]; # <x>
$m[3] += $d*$p[0]; # <x^2>
$m[6] += $d*$p[1]; # <xy>
$m[7] += $d*$p[2]; # <xz>
$m[1] += $d = $mass*$p[1]; # <y>
$m[4] += $d*$p[1]; # <y^2>
$m[8] += $d*$p[2]; # <yz>
$m[2] += $d = $mass*$p[2]; # <z>
$m[5] += $d*$p[2]; # <z^2>
}
pdb_center(M_Mult(1/$nmass, @m)) if ($nmass);
pdb_focus(M_Mult(1/$nmass, @m)) if ($nmass && scalar(%focus));
pdb_pbc() if (scalar(%pbc));
pdb_repair_bonds() if ($repair);
}
sub pdb_header
{
printf(PDB "REMARK \n");
printf(PDB "REMARK ".$project."_trj.pdb GENERATED FROM ".$project.
($psf_ctrl ? "_ctrl.psf" : ".data")." AND $project.dump\n");
printf(PDB "REMARK CREATED BY $program v$version ON %s", `date`);
printf(PDB "REMARK \n");
printf(PDB "CRYST1 ");
printf(PDB "%8.8s ", $l[3]);
printf(PDB "%8.8s ", $l[4]);
printf(PDB "%8.8s ", $l[5]);
printf(PDB "%6.6s ", "90");
printf(PDB "%6.6s ", "90");
printf(PDB "%6.6s ", "90");
printf(PDB "%-11.11s", "P 1");
printf(PDB "%3.3s\n", "1");
}
sub pdb_atoms
{
my $n = 0;
my $l = 0;
my $last = 0;
my @base;
pdb_positions();
psf_goto(atoms) if ($psf_ctrl);
printf("Info: writing positions for timestep %d\n", $description[0])
if ($info);
foreach (@position)
{
my @p = split(" ");
my $nres = $mol[$p[3]];
my @psf = split(" ", advance_read(PSF_CTRL, $p[3]-$l))
if ($psf_ctrl);
@base = @p[0,1,2] if ($last!=$nres);
#@p = V_Add(V_PBC(V_Subtr(@p, @base), @l[3,4,5]), @l);
foreach (@p) { $_ = 0 if (abs($_)<1e-4); }
printf(PDB "ATOM "); # pdb command
printf(PDB "%6.6s ", ++$n); # atom number
printf(PDB "%-3.3s ",
$psf_ctrl ? $psf[4] : $names[$p[4]]); # atom name
printf(PDB "%-3.3s ",
$psf_ctrl ? $psf[3] : $residue[$nres]); # residue name
printf(PDB "%5.5s ", $nres); # residue number
printf(PDB "%3.3s ", ""); # empty placeholder
printf(PDB "%7.7s %7.7s %7.7s ",
$p[0], $p[1], $p[2]); # positions
printf(PDB "%5.5s %5.5s %4.4s ",
"1.00", "0.00", ""); # trailing variables
printf(PDB "%-4.4s\n",
$psf_ctrl ? $psf[1] : $cluster[$nres]); # cluster name
$last = $nres;
$l = $p[3];
};
printf(PDB "END\n");
}
sub pdb_timestep
{
pdb_header();
pdb_atoms();
return ();
}
# psf format
sub psf_header
{
printf(PSF "PSF\n");
printf(PSF "\n");
printf(PSF "%8.8s !NTITLE\n", 2);
printf(PSF "REMARK ".$project."_trj.psf GENERATED FROM $project.data\n");
printf(PSF "REMARK CREATED BY $program v$version ON %s", `date`);
printf(PSF "\n");
}
sub psf_atoms
{
my $n = goto_data(atoms);
my $natom = 0;
my $l = 0;
my $k = 0;
my @extra;
for (my $i=0; $i<$n; ++$i)
{
my @arg = split(" ", <DATA>);
if (!$k) {
for ($k=0; ($k<scalar(@arg))&&(substr($arg[$k],0,1) ne "#"); ++$k) {} }
$extra[$arg[0]-1] = $arg[1]." ".$arg[2]." ".$arg[3];
}
printf(PSF "%8.8s !NATOM\n", scalar(@position));
foreach (@position)
{
my @p = split(" ");
my @arg = split(" ", $extra[$natom]);
printf(PSF "%8.8s ", ++$natom); # atom number
printf(PSF "%-4.4s ", $cluster[$arg[0]]); # cluster name
printf(PSF "%-4.4s ", $arg[0]); # residue number
printf(PSF "%-4.4s ", $residue[$arg[0]]); # residue name
printf(PSF "%-4.4s ", $names[$p[4]]); # atom name
printf(PSF "%4.4s ", $arg[1]); # atom number
printf(PSF "%10.10s ", $k%3 ? $arg[2] : 0); # atom charge
printf(PSF "%4.4s ", ""); # blank entry
printf(PSF "%8.8s ", $masses[$arg[1]]); # atom mass
printf(PSF "%11.11s\n", "0"); # trailing variable
$l = $p[3];
last if ($natom>=$n)
}
printf(PSF "\n");
}
sub psf_bonds
{
my $npairs = 0;
delete_exclude() if (scalar(%exclude)>0);
delete_crossovers() if ($cut);
printf(PSF "%8.8s !NBOND\n", scalar(@bonds));
foreach (@bonds)
{
my @arg = split(" ");
printf(PSF " %7.7s %7.7s", $arg[0]+1, $arg[1]+1);
if (++$npairs>=4) { printf(PSF "\n"); $npairs = 0; }
}
if ($npairs>0) { printf(PSF "\n"); }
printf(PSF "\n");
}
# main
initialize();
# create .pdb file
$ncurrent = -1;
while ($traject_flag&&!eof(TRAJECT))
{
@description = read_traject();
@l = splice(@description, -6, 6);
next if (($nstart<0)||(++$ncurrent<$nstart));
if ($dn<1) { pdb_timestep(); last; }
$ncurrent = pdb_timestep() if ($nstart||!($ncurrent%$dn));
$nstart = 0;
}
pdb_timestep() if ($nstart<0);
# create .psf file
if (!$psf_ctrl)
{
psf_header();
psf_atoms();
psf_bonds();
}
else
{
system("rm -f ".$psf_name);
system("ln -s ".$psf_ctrl_name." ".$psf_name);
}
# add tail to files
#printf(PDB "END\n");
printf("\n") if ($info);
close(PDB);
close(PSF);
close(TRAJECT);
close(DATA);

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